A New Life
by twi360amylouise
Summary: What happens when SG1 leave earth and Atlantis is cut off for good? And how do Rodney and John react to Jeannie now living in Atlantis? Story now discontinued.
1. Chapter 1

AN: So i have read a lot of stargate fanfiction since my cousin got me into it. i thought i would try to write a fic so here it is let me know if i should continue or not.

I don't own anything unfortunatley.

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John and Rodney were slowly walking through the corridors of Atlantis when they both heard Woolsey over the radio asking them to report to the gate room. They turned back the way they had come rather reluctantly to see what the next disaster was that they had to fix. When they got there, they saw that Woolsey was still stood at the computer screen where they had left him to the fortnightly check in with Earth. He turned around as he heard both Rodney and John approaching and his jaw was clenched as were his fists at his side.

"Gentlemen I am afraid I have some bad news."

"Go on, just get it over with." Rodney said impatiently, tapping his fingers on the nearby control station.

"Earth is officially cutting us off. They are not very happy with the decisions that have been made by any of the leaders in command here and have decided it would be best to discontinue the expedition. You are welcome to go back to Earth if you desire once the Daedalus has reached Atlantis it is to unload and then go back to pick up the last batch of supplies. Same with the Apollo anyone who wishes to go back to Earth is to be on either of the ships and the Daedalus is bringing the original SG1 back as they have asked to come here along with doctor Frasier and Cassandra, there will be a city wide announcement to come to the gate room sent out in a minute and I wanted both of you to know before everyone else."

"They are cutting us off because of a few bad decisions?" Rodney asked with an exasperated sigh.

"The original plan was for everyone on Atlantis to return to Earth but then I argued the point that this is now home for many people and they would not return, so the IOA gave the option of returning or being cut off."

Rodney looked to John "Are you going to go back?"

"No of course not, Woolsey is right, this is home now. Are you going to go back?"

"I am not thinking about it but then there is Jeannie, I have only just got back in contact with her."

"If she would like to, we can have her brought on the Daedalus with SG1. Her and her family, so she wouldn't be alone unless there is anything keeping her on Earth." Woolsey said.

"Is there another check in with Earth before this happens?"

"Yes there will be one in an hours' time."

"Great. How long will the gate be open?"

"Well the gate will have to be dialled again at least once during the check in so at least about an hour."

"Great while the gate is open I can ring Jeannie and explain to her what is happening and then if she agrees we can start sorting out quarters for the new arrivals. "

Just then the city wide announcement went out.

Slowly everyone filtered into the gate room where Ronon and Teyla approached John and Rodney. "What's going on?"

"The expedition is being cut off from Earth because of a few bad situations and the decisions made in them, but wait, they are going us a load of supplies as well as SG1 and the Daedalus and the Apollo." Rodney answered sourly with a tight lipped smile.

Just then Woolsey started speaking. "Can I have your attention everyone? Thank you. Right well, i have an important announcement to make. Atlantis is being cut off from Earth. The Apollo and the Daedalus will be making one more trip and then Earth is having nothing more to do with Atlantis. The Daedalus and Apollo are willing to take back anyone who would like to return to Earth but you must consider this is a one way trip, for those of you who know you definitely want to stay you are more than welcome, there will be a check in with Earth within the next hour so if anyone has a phone you will be able to call loved ones, friends anyone you wish to say goodbye to. For anyone that wants to return back to Earth you have until 10 o'clock tomorrow morning to pack your things and be here to be beamed up onto the Apollo. I would like anyone staying to convene back here at 6 o'clock tomorrow evening. Thank you."

John, Rodney, Teyla and Ronon headed to the mess to grab something to eat quietly discussing the new development between themselves.


	2. Chapter 2

They grabbed their food and chose a table on the balcony away from everyone else. It was Teyla who spoke first.

"Are you going back to earth?" she asked softly.

"Of course not this is my home now. I don't have anyone on earth apart from Dave and he doesn't want to know me so I am staying here." John said with a smile.

Teyla turned to Rodney. "What about you Rodney?"

"Huh, no I am staying and hopefully I can convince Jeannie and Kaleb to come out here on the Daedalus."

The rest of the time was spent talking about their last mission until it was time for the check in.

Rodney was briskly pacing across Woolsey's office; he was waiting for Chuck to dial the gate so he could speak to his sister. He heard the whoosh of the gate and started dialling her number. It rang for a few minutes before Jeannie finally answered.

"Hello?"

"Jeannie!"

"Meredith! Where are you? How are you calling?"

"I am still in Atlantis and the gate is open giving us a connection."

"Okay is there any particular reason you called?"

"Yes I'm just going to come right out and say it. The IOA decided they want nothing to do with Atlantis and are cutting us off after the next Daedalus run."

"Wow! So are you coming home?" Jeannie asked tentatively.

"Yeah that's the thing. I have chosen to stay in Atlantis but with being the head of the science department Woolsey said he can get you, Kaleb and Madison onto the Daedalus when it comes back if you want to."

"Really? Hang on what's the catch?"

"You have to decide within the next half an hour."

"Half an hour!? Mer that's not very long."

"I know."

"I will talk to Kaleb about it and will ring you back in twenty minutes okay?"

"Okay."

Rodney hung up and started to pace the gate room again and he only stopped when John put his hand on his shoulder to stop him. He then pulled Rodney into a reassuring hug.

"It will be fine I promise. She will choose to come to Atlantis I know she will."

"Thanks."

John was cut off from replying by Rodney's phone ringing.

"Hello?"

"Hey Mer it's me. We decided, well, I decided we would love to come we have only just got back in touch and I would hate to lose you forever."

"Right. Can you remember Sam?"

"Yeah. Why?"

"Well she is coming with you, well all of SG1 are actually but you have only ever met Sam, anyway she will help you and will get you into the mountain to be beamed aboard the Daedalus okay?"

"Okay"

"I guess I will see you soon then."

"Yeah, bye Mer."

"Bye."

Rodney hung up and turned to face John.

"She's coming. She said she couldn't stand it if we lost contact again after just getting back in touch."

"That's amazing Rodney, it really is, but we have one problem."

"What?"

"Well your sister is coming to live on Atlantis and you still haven't told her about us. How the hell do you think we are going to be able to keep it a secret when everyone here already knows?"

"I didn't think of that. I will have to think of a way to tell her in the next couple of weeks while she is on the Daedalus."

Together they headed out of the gate room and up to Rodney's quarters, where they sat and talked about what was going to happen now, and how they were going to tell Jeannie. Early the next morning, they headed back to the gate room to see if anyone turned up to go back to earth and to both of their surprise Jennifer was stood talking to Woolsey with all of her things packed behind her.

"Jennifer? I thought you would be staying." Rodney said as they approached.

"I would love to, but my dad is terminally ill and I have to go back to take care of him. I know there is no chance that I will be able to come back but I have to see him."

"Actually there might be a way to get you back, if you want to come."

"How? You never mentioned this before." Woolsey said pointedly looking at Rodney with narrowed eyes.

"Because I only just thought of it. I can give you a sensor that if you activate will alert us that you want to come back. We could then come on the Daedalus or the Apollo and get you by beaming you up on board."

"But won't you be detected by sensors on Earth?"

"No because between Sam and i we should be able to deactivate them or at least cause a malfunction considering we designed them."

"That's great Rodney that gives us away to get supplies that we may need from Earth as well." John said looking at him proudly.

"Thanks. We also adapted the device so it works across both galaxies not just the Pegasus which means we will definitely get the signal."

"We?" John asked surprised.

"Zelenka may have helped a little."

Just then Colonel Ellis radioed down to say they were ready to accept anyone going back to earth. Jennifer gave both Rodney and John a hug and then nodded to Woolsey after receiving the transmitter of Rodney. Woolsey radioed Ellis telling him that Jennifer was ready to go and she was gone in a flash of light. Rodney headed down to the lab and John headed to the gym to spar with Ronon. They spent a few hours in the gym before going to clean up and grabbing Rodney and Teyla with Torren to get something to eat. It was very rare to not see AR1 not sitting together in the mess.

"So will you miss anything on earth?" Ronon asked.

"Ferris wheels." John replied seriously.

"Ferris wheels?" Rodney asked disbelievingly.

"I like Ferris wheels okay." John replies putting his hands up in defence.

"Okay apart from these Ferris wheels is there anything else? Any family?" Teyla asked to calm them both down.

"My cat!" Rodney exclaimed suddenly remembering it.

"Your cat Rodney?" Teyla asked tilting her head to one side.

"Yes, oh sorry a cat is a little animal, full of fur and it just sits around all day."

"If it just sits around all day why would you want one?" she asked still confused.

"Because they are great companion. And no I don't have anyone I would miss because Jeannie is coming here."

Teyla looked to John. "Didn't you say you had a brother once?"

"Yeah but we don't speak to one another, he made it quite clear at my father's funeral that he wanted nothing to do with me and couldn't care less about where I am so it's his loss."

"Are you not even going to try and make peace with him before we get cut off and you never get the chance?"

"I will get the chance if I want, Rodney has devised a way to be able to go to Earth should we need to."

"Really?" Teyla asked surprised.

"Yeah, we just go on the Apollo or the Daedalus and use the beaming technology to get someone down who can then get supplies or whatever."

"But doesn't your world have some sort of sensor system to detect oncoming space ships."

"Yes but, the great thing about that is that they were all designed by Sam and i meaning we can either deactivate them or causes a malfunction that will not show."

"Colonel Carter is coming back to Atlantis?" Ronon asked.

"Yeah and the rest of the original SG1, they decided that because we are being cut off they want to come here." John replied.

The team finished up their meal and headed their separate ways to their quarters. John and Rodney spent a while talking about Jeannie and about what the appearance of SG1 meant ,and if John would have to give up the title of head of Atlantis military to Sam or jack as they were both more experienced than him and had higher ranks.


	3. Chapter 3

Okay, so the idea of a database full of movies and TV shows and books and games from earth was not mine and full credit for the idea goes to JanusGodOfPossibilities because to be honest I hadn't really thought about it. So yeah, hope you enjoy the chapter.

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Before the city wide announcement went out the team spent the day together watching movies from the database that Sam had put together containing a large collection of popular movies, tv shows, books, games and anything relating to Earth that would be of use or entertain the members of the expedition. Together they headed to the gate room just before the city wide announcement. John slowly made his way into Woolsey's office where he saw him just staring at the tablet in front of him with his head rested on his clasped hands in front of him.

"Are you alright sir?" John asked tentatively.

"What? Oh yes I am fine just wondering what is going to happen when Colonel Carter and General O'Neill get here. Right I will go and send out the announcement for everyone to come to the gate room."

Fifteen minutes later and the gate room was filled with Atlantis personnel.

"As you all know we are being cut off from Earth. I have just received an email today to say that Doctor Beckett will be allowed to return to Atlantis with SG1. As some of you might have noticed our current chief of medicine is not here and that is because Doctor Keller decided to return to Earth due to personal circumstances. As to what we do now that we have no contact with Earth, I want you to go about your jobs as you would normally, this time however, we get to keep everything that we find to fight the wraith. There will be a further meeting just before the Daedalus and the Apollo arrive back to discuss what will be happening with the arrival of SG1. That is all for now you are dismissed but could Major Lorne stay behind. Everyone started leaving the gate room and going back to their jobs and Evan made his way up to Woolsey's office where John, Rodney and Woolsey were.

"Sir?"

"Yes, Evan I would like you to work with Colonel Sheppard and Doctor McKay to sort out and furnish the appropriate quarters for our new arrivals until then I am taking AR1 off of active gate duty and I will have someone fill your spot on your team Major."

"Yes sir." Evan turned and left to go inform his team they would be working without him for a few weeks. Woolsey turned to John and Rodney "may I advise that you consult Teyla for help with furnishings." Rodney and John left Woolsey's office to go and see if there were any major incidents in the lab while Rodney was gone. When they entered the lab they saw Zelenka getting quite agitated with some poor scientist because he had apparently just caused something to blow up. Just as Rodney was going to intervene the power went out.

"Seriously I was gone for ten minutes and you managed to break something." Rodney exclaimed angrily throwing his hands in the air. He walked out the door and grabbed John's arm on the way dragging him along with him.

"Where are we going?" he asked after he had gotten his arm back from Rodney.

"To the chair room to see what damage has been done and how we can fix It." They entered the chair room and Rodney pushed John over to the chair.

"Sit. Tell me what you see." he said rather harshly.

"The explosion in the lab blew out the lights which led to the rest of the power cutting itself off."

"Great just another problem we have to fix." Rodney exclaimed exasperatedly. "Is there any way that you can reroute the power from the lights so everything else will hopefully come back on?"

"I have no idea how I would do that Rodney maybe you are better off in the chair."

"Fine." John got up off the chair and Rodney took his place. He sat for five or six minutes rerouting the power and seeing if there was anything else he could do to fix the problem from the chair room. When he determined that there was no more he could do he radioed Zelenka.

"Zelenka come in,"

"Yes Rodney?"

"I have rerouted power away from the lights so everything should come back on and it looks like the wiring in the lad in the lighting is going to need replacing."

"Okay we will get to work right away."

Rodney and John headed down to the mess to get something to eat and found Teyla, Ronon and Torren already at a table in one of the far corners.

"Hey guys what you been up to?" John asked when they sat down.

"We went for a walk around the mainland this morning and went to visit some of my people."

"Sounds good."

"It was what you did?" she asked politely.

"Oh you know just fixing Zelenka's mistakes." Rodney replied.

The team finished up their meal and then headed back down to John and Rodney's quarters for movie night and the movie that night was Serenity. They spent most of the night John and Rodney answering all the different questions that Teyla and Ronon had about the movie. It eventually finished and Ronon and Teyla went back to their quarters to see to Torren. John and Rodney settle down for the night and talk about the task they had been given by Woolsey. They decided that they would leave the decorating to Teyla as she had the feminine touch.

The next morning Rodney gets up and heads down to lab to see Zelenka giving orders to the other scientists. He clears his throat and Radek turns around to look at him.

"Rodney! What are you doing here? Mr Woolsey said that he has taken you of duty for the next few weeks."

Rodney turned back around and headed for the control room and Woolsey's office.

"I can't even set foot in the lab that I work in?" he asked as soon as he entered the office.

"I did tell you yesterday doctor that I was taking you off of active duty for the next few weeks."

"And that includes the lab?" Rodney asked

"Yes it does I want your full attention on preparing the rooms for our new arrivals"

"But we have three weeks!"

"Yes and your three weeks will be dedicated to making sure that the quarters are appropriately decorated." Rodney turned around and stormed out of Woolsey's office and to his quarters where he flopped on the bed and grumbled about Woolsey and not being able to do his job. John entered their quarters some time later to find that Rodney had fallen asleep he gently shook him awake and they headed to the mess to get something to eat. After they had lunch with Teyla Ronon and Torren they all headed up to the rooms that had been assigned to SG1 and Jeannie. The quarters had never been used before and had pieces of thousand year old furniture still in them. Ronon and John emptied the room of the old furniture and took it to a storage room at the end of the hall where it would stay until they could figure out what to do with it. While Ronon and John were moving furniture Rodney and Teyla were cleaning out the old kitchen cupboards and getting everything ready for when the supplies arrived on the Apollo. They done this in all five quarters, they also sat down with Teyla and discussed what furnishings would go in each room and what colour they would be. After a long afternoon of working and cleaning they headed back to the mess stopping to get Torren from Lieutenant Cadman who had offered to watch him for the afternoon. They headed their separate ways after they finished their meal to get a good night's sleep for the decorating they were going to be doing tomorrow after the Apollo had dropped off its supplies and restocked.


	4. Chapter 4

Hey peoples, so I said I would update with another chapter and here it is. Sorry if its a bit boring :):)

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The next morning John and Rodney got up and headed straight to the docking bay where they waited for the Apollo to arrive. When Ellis arrived with the Apollo, he beamed down the furniture that had been brought for the new quarters into the designated empty storage room at the end of the corridor, where the new quarters were located in the city. John and Rodney gathered all the paint onto a trolley that they had brought from one of the labs so they didn't have to carry it all the way across the city they then used transports to get to the rest of the way to where Teyla and Ronon were waiting patiently for them. When they reached their destination, Ronon helped them to unload the paint and Teyla started telling them which rooms to place the paint tins in.

"The blue goes into the bedroom please and the red goes into the spare room, the white goes into the kitchen and the bathroom and the green goes into the main room. The grey goes into the dining room please." They each took the different colours and placed them in the correct room. Teyla then took John and Rodney into the main bedroom and told them that the wall opposite the window needed to be blue, and the rest of the room was going to be white. Rodney started painting the main wall, while John started painting the other three. Teyla and Ronon started painting the spare room in the same way just red instead of blue half way through their painting John and Rodney got into a paint fight and ended up both covered head to toe. Ronon and Teyla went in to see what was going on and were both bombarded paint.

"What was that for?" Ronon asked grufly.

"It's called starting a paint fight." John replied grinning until Ronon upended a pot of paint over his head. Rodney done the same thing to Teyla and they all ended up laying on the floor laughing. John and Ronon headed to the mess to pick up lunch for all four of them and they got quite a few funny looks because of the paint they were splattered in. While they were in the mess, Woolsey came and asked how much progress they had made.

"We have finished painting the first half of the quarters that will belong to Colonel Carter and General O'Neill, we should have them finished by the end of the day and then we will move on to the others tomorrow."

"That's good to hear." Woolsey said and then walked off towards his office. John and Ronon grabbed the sandwiches and coffee for the dinner and headed back to the quarters where Rodney and Teyla were just finishing up the last of the painting in the rooms they were in. They both re-emerged from their respective rooms when they heard John and Ronon enter. The group continued to paint the rooms with the help of Evan over the next few days and were glad when all the painting was done. Each set of quarters were decorated in relation to who would be living in them and the quarters that were put aside for when Cassie decided to leave Daniel and Janet's rooms and move into her own. They decided to take the weekend off after working through the week. Teyla and Ronon took Torren over to the mainland to spend the night with Teyla's people, while John and Rodney spent most of the weekend talking about Jeannie and how they were eventually going to tell her that they were in a relationship. They finally decided that they would just tell Jeannie two of three days after everyone had settled in. Monday morning found Teyla, Ronon, John, Rodney and Evan back in the newly painted quarters this time trying to figure out where the furniture was going to go and which pieces of furniture were going to go in which room. Ronon and Evan were tasked with carrying the furniture from the supply cupboards to the quarters and then John and Rodney were given the job to arrange the furniture in the room where Teyla wanted it.

The next week was filled with, much of the same and several failed attempts to get into the lab on Rodney's part. The team spent a relaxed weekend together anticipating the arrival of the newcomers on Monday morning. On the Sunday before the new arrivals were due to arrive Woolsey met the team in gate room so he could go and inspect the newly decorated quarters. He was quite pleased with the way that Teyla had designed everything and gave the team the entire week off and permitted Rodney to enter the lab and finish some research that he was working on.


	5. Chapter 5

_I don't own anything unfortunatley._

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Later in the evening Woolsey made a city wide announcement. John Rodney Teyla and Ronon were the first to arrive and Woolsey used the next fifteen minutes to explain an email he had just received off of General O'Neill. When everyone was gathered he stood on the balcony with AR1 behind him and addressed the personnel.

"I have not long received an email of General O'Neill about what roles the SG1 want to undertake.

Colonel Carter, Doctor Jackson and Dr Miller would like to work closely with the science department. Doctor Frasier would like to work in the infirmary alongside Doctor Beckett who will return as the chief of medicine. Teal'c and General O'Neill have expressed an interest in participating in training the military."

Monday morning saw John moving some of his things back into his old quarters, he wasn't moving much but enough so that it looked like he was staying there and not in Rodney's quarters as he had been. He and Rodney had agreed that until they told Jeannie it was best to stay in separate quarters. After he was finished John slowly made his way down to the labs where Rodney was working and collected him so they wait in the gate room for the new arrivals to be beamed down from the Daedalus. John stood patiently next to Woolsey who stood with his arms crossed facing the gate. Rodney stood a little bit behind them with Ronon, Teyla and Torren. At 11 am exactly there was a beam of white light and all 9 new personnel members were stood in front of them, the marines who normally stood guard in the gate room moved forward and took the luggage up to the relevant quarters. After introductions were made to the people who didn't know each other John showed Sam, Jack, Daniel, Janet, Cassie and Teal'c to their quarters while Rodney walked Jeannie, Kaleb and Maddison to theirs. Once they had unpacked Rodney showed them around and then made a quick retreat to the lab where he immersed himself in his work. Jeannie and Kaleb had decided to go back to their quarters to finish unpacking and settling in. John joined Rodney in the lab after he had shown Janet and Cassie around. They tried to be as normal as possible but with the very real possibility that Jeannie could walk in at any time they put enough distance between each other to not be suspicious and they kept the topic of the conversation to work or idle chit chat. When it was time to go get something to eat Rodney went to get Jeannie, Kaleb and Maddison while John went to get Teyla, Ronon and Torren. They all met up at the mess hall where Rodney introduced them to the rest of the team, with Jeannie and Teyla instantly hitting it off. Kaleb was still wary around Ronon even though he saw how gentle and careful he was with Torren and knew that he wasn't as intimidating as he seemed, all the time. Dinner went fairly well and after they finished Rodney showed Jeannie to the labs. Rodney worked out how Jeannie would fit into the team and then they went their separate ways with Jeannie going back to her quarters and Rodney staying in the lab to get a report of Zelenka. Rodney arrived back at his quarters and just lay on the bed thinking about how strange it was to be alone in his quarters once more. He sat up and carefully looked around the room missing all the little things that reminded him of John's presence, it had only been a few hours since he had moved his possessions but it already felt lonely and empty without him there. Unknown to Rodney, John was feeling exactly the same way across in his old military quarters. He tried to read a book and listen to music but it just wasn't the same as listening to Rodney's random rambling. After a few hours of feeling sorry for himself John took the life signs detector out of the pocket of his tac vest that he still hadn't taken back to the locker room and decided to go see Rodney. It took him fifteen minutes to reach their quarters without being seen and when he got there he found that Rodney had fallen asleep on top of the covers on the bed. He gently shook Rodney awake and managed to get him in the bed properly before climbing in beside him and finally letting himself fall asleep. Rodney woke up the following morning to see John still fast asleep beside him even though he shouldn't have been there. Just as he was going to wake him up, the door chimed indicating that there was someone outside. Rodney hastily shook John awake and told him to go hide in the bathroom, he sleepily complied once he understood the nature of the situation and Rodney answered the door. Jeannie was standing on the other side with an impatient look on her face.

"Nice of you to open the door"

"I was asleep what do you expect me to do jump up and answer straight away? Anyway what do you want?"

"Zelenka needs your help on one of the projects but he couldn't get through on your radio."

"Okay I am coming give me two minutes."

Jeannie turned and started walking back to the while Rodney went back into the quarters and told John he could come out from the bathroom.

"What are you doing here anyway?" he asked confused.

"It was strange and lonely in my old quarters."

"So you decided to risk coming back here?"

"I used the life signs detector to make sure I didn't run into anyone in case Jeannie or anyone from SG1 were wandering the halls."

"About that I think we should just tell her."

"Are you sure, I mean I don't have a problem but she's your sister."

"I know and if she decides not to accept it then so be it."

"Rodney are you completely sure?"

"Why not? We didn't speak for four years before we needed her help here in Atlantis; it really wouldn't bother me that much to be not speaking, I can go however long without speaking to her just because she doesn't like who I am John. I accepted that she left the world of science to get married and have a kid, I may not have liked it and may have complained and try to persuade her against it and although we fell out over it I came to accept it. Whether she knows it or not."

John walked over to him and gave him a hug before heading to the briefing that Woolsey had called for the heads of the relevant departments about SG1

"I'll tell Woolsey you were called to the lab and not to start the briefing without you." he called over his shoulder as he left. Rodney got dressed and headed down to the lab to see Zelenka working quietly at a computer.

"Jeannie said you needed help on a project?" Rodney asked as he walked up to Zelenka.

I am not currently working on anything new." Zelenka replied looking a little taken back.

Rodney walked out of the lab and made his way to the conference room for the meeting. When he got there they waited for him to take his seat next to John and then Woolsey asked

"Is everything okay Doctor McKay?"

"What oh yes Zelenka has it under control."

"Okay let's get on then. Doctor McKay, Colonel Carter has requested that she would like to work within the science department. Is that possible?"

"Yeah of course" he answered distractedly.

"Mrs Miller had also requested to work in the science department is that also possible?"

"Yes we have already worked it out and I am sure we will also be able to find a position for Doctor Jackson. "Rodney replied.

"Thank you Doctor McKay. Now Colonel Sheppard is it possible for Colonel Carter to also be involved in the military aspect of Atlantis?"

"We could assign Colonel Carter to a team so she gets to go through the gate and work with science."

"That would be great thank you."

"We could also assign Teal'c to a team to keep him involved with the military aspect and he could also help Ronon with training the marines."

"Thank you Colonel and as for General O'Neill it is up to him I suppose but I am guessing he will be involved in training the marines as well. There is also the option that they are assigned as a team but they also help out in each of their specialist areas."

"That would be fine with me, as long as they don't take our place as AR1, and they understand that although they may outrank me they are still under my command."

"I am sure they will have no problem accepting that colonel." Woolsey said before turning to Carson.

"Doctor Beckett is there some way in which Doctor Frasier could possibly work within the infirmary?"

"Certainly. I will be glad for the extra help to be honest." Carson replied. Woolsey nodded and dismissed the meeting saying he would hold a meeting with SG1 to let them know of their positions within Atlantis.


	6. Chapter 6

AN: I know I said I would try and update at least every fortnight and I am sorry that I haven't updated sooner. There really is no excuse so I hope you enjoy and as usual don't own anything.

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Everyone left the meeting and Rodney headed down to the labs while John headed to his office to fill in the relevant paperwork, he had to fill in the forms for a new team to be formed and all the equipment they would need for their missions. He also had to fill in the some mission reports from previous missions they had been on, as well as sorting out accommodation for Colonels Caldwell and Ellis and their crews. It would be nothing fancy, just standard personnel quarters but they would have to stay on board their ships until he could sort it out and at least he had another 6 weeks to work something out, or he would assign the task to one of the marines. John suddenly had an idea and left to go see Woolsey. Slowly he walked to his office and knocked on the door; he entered when Woolsey looked up and beckoned him in.

"Is there something I can do for you colonel?" Woolsey asked.

"I had an idea. I think we should send major Lorne with the Orion to Earth to stock up on supplies as well as the Daedalus and Apollo."

"Are you sure about this Colonel? It would leave us with a very limited supply of marines in case anything happened."

"I know but between us I am sure we will be able to spare the Orion for a week if we send it ahead equipped with one of the spare ZMPs."

"I will talk to Stargate Command and see what their opinion is. Thank you for letting me know." John stood up and went back to his office to finish filling in the paperwork he had started. About half an hour later he heard the door chime to inform him that there was someone there. Absentmindedly he beckoned for the door to open and was surprised to see Rodney standing on the other side.

"Rodney? What's wrong?" he asked seeing the look on his face.

"It's Jeannie." he replied while walking into the office and sitting down

"What do you mean?" John asked worried that something had happened to her.

"I went to the lab this morning after I left our quarters and asked Radek what he needed help with and he said that he wasn't currently working on anything that he required help with."

"What do you mean he wasn't working on anything? I thought that you were always working on something in the labs"

"We are but Radek looked completely shocked to see me and was slightly taken back when I asked him about what he needed. Come to think, of it Jeannie wasn't in the lab either." He said looking at John for the first time his face going pale white.

John groaned and threw his pen down in the desk while scrubbing his hand over his face. "You don't think?"

"Think what?"

"No offence to Jeannie, Rodney, but i left this morning not five minutes after you left. You don't think she told you Radek needed you to get you out of the quarters and then waited to see if anyone emerged after you, do you?"

"Right now I don't know what to think. Especially if she made it up, she has really changed if she did."

"What are you going to do?" John asked quietly.

"Ignore her for the rest of the day and see what happens tomorrow I don't know what else to do."

"Come on then." John said standing up and pulling Rodney to his feet.

"We'll go back to our quarters, get Teyla and Ronon to bring something to eat and we will all watch a movie to keep your mind off of it for now." They both left John's office and the walk through the halls of Atlantis was quiet apart from John talking to Teyla and Ronon over his radio. When they got back to their quarters, Rodney chose Independence Day to watch while John just shook his head and rolled his eyes. A few minutes' later Teyla and Ronon showed up with the food and some popcorn and they all settled in to watch the movie. Throughout the movie John's thoughts strayed to Jeannie and why she would put Rodney and Radek in the situation she did and he decided that the next chance he got, he would go and see her. He didn't tell Rodney as he knew he would kick up a fuss and tell him to leave it alone. By the end of the movie it was still early but Rodney had fallen asleep so Ronon helped John get him onto the bed then Ronon and Teyla headed out to go spar while John sat at his desk in their quarters for a while. He couldn't concentrate on his work any longer so after checking on Rodney, he left their quarters and went to find Jeannie. Atlantis guided him to where she was and he found her in a conversation with Carson, he was just about to walk over when he heard the conversation take a different turn.

"What's going on between Colonel Sheppard and my brother?" he heard Jeannie ask as he thoughts strayed to how he was right that she suspected something.

"I don't know what you're talking about lass." Carson replied.

"Oh come on Doctor Beckett you're his best friend you must know something." Jeannie replied.

"I'm afraid I don't lass and if there was something going on you should trust Rodney to tell you himself."

"Fine, see you later doctor Beckett." Jeannie replied before heading out of the door and back to the lab. Just as John was about to go and talk to Carson, Woolsey summoned him to the gate room. He quickly made his way there, and once he arrived he saw Woolsey standing next to Chuck the gate technician at the control panel for the gate.

"Colonel Sheppard, I need you to take AR1 to go and find major Lorne's team, they left this morning and they have missed their check in by 3 hours." Woolsey said when John was stood next to him.

"Understood sir, I will go and round up the rest of the team." John said and then turned and left the gate room. He made his way back to his quarters where he woke Rodney up and then headed to the gym to get Ronon and Teyla. Together the made their way to the locker room where they geared up for the mission. Within fifteen minutes they were back in the gate room and were watching the gate activate. John could see Jeannie standing up on one of the balconies watching him out of the corner of his eye, he shook off the feeling of uneasiness and lead his team through the gate. It turned out that Lorne and his team had been captured by the locals for a simple misunderstanding and after a conversation, John put things right and the natives released Lorne and his team letting them return to Atlantis. Once back in the ancient city the gate cut off and John was just about to order Lorne's team to the infirmary to get checked out when Rodney collapsed.


	7. Chapter 7

John was instantly by his side and was ordering a med team to the gate room. Carson arrived a few minutes later and lifted Rodney onto the stretcher and took him to the infirmary. John followed a few minutes later, after giving Teyla his weapon and his TAC vest. Rodney was unconscious for quite a few hours and John sat silently besides his bedside patiently waiting for him to wake up. Throughout the time he was sat there, Jeannie didn't once visit Rodney so after a while John got up and went to find her. He decided to check the lab first as that was where she was most likely to be. When he arrived, he saw that she was in a conversation with Radek that from the outside looked uncomfortable. Before Radek could answer the question that had just been asked John walked into the room.

"Jeannie can I talk to you a minute?" he asked pulling her to one side.

"Sure what is it?" she asked a little surprised.

"Rodney has been in the infirmary for hours now and you haven't been to visit?" he asked with anger in his tone.

"I have been I just didn't stay long." Jeannie said with impatience as she tried to create a believable cover story.

"Don't lie to me Jeannie, if there is one thing you don't do it is lie to my face. I have been in the infirmary since we came back through the gate and you haven't visited once. Why? Do you really resent your brother that much that you won't visit him?"

"Why have you been sitting in the infirmary? Why did you not come and get me?"

"Don't turn this back around on me. I am the leader of the groups and therefore he is under my command. And did you ever stop to think that maybe your brother has friends here?"

"Friends? What's really going on between you? I know you are more than just friends I saw you coming out of his quarters the other morning?"

"That's up to Rodney to tell you not me but that still doesn't explain why you haven't been to see him in the infirmary."

"He'll be fine, he always is."

"But that's the thing Jeannie you don't know, you have no idea what could have happened off world. You haven't been to see him or anyone else from the team to find out what actually happened. Pegasus is a dangerous place Jeannie and every time we step through the gate there is a chance we won't come back. The quicker you realise that the better."

John finished speaking and then without waiting for a reply he turned around to head back to the infirmary. By the time John got back to the infirmary, Rodney was awake and talking to Carson. Luckily he hadn't said anything about his conversation with Jeannie. John tried to hide the anger but he knew Rodney saw before he managed to put a smile on his face.

"Hey. How are you feeling?" John asked in a concerned tone.

"Fine but Carson won't let me leave." Rodney complained.

John walked over to Carson. "Hey Carson can Rodney leave yet?"

"If you take him back to your quarters and make sure that he rests then I suppose he can. I will come and check on him later."

John walked over to Rodney's bed and gave him the good news.

"Doc said you can leave if you rest in our quarters and he will come and check in on you later."

"That's fine I just want to get out of here." Rodney got up and got dressed before they headed out of the infirmary and down to their quarters. Rodney tried to go and get his laptop to finish some work but John stopped him and forced him to sit down on the sofa and watch a movie again, staying with him so he didn't try to do work. As promised Carson stopped by after he had finished his shift in the infirmary, he checked Rodney over and said he was fine but he had to rest for the next two days and that included not going into the lab. Just as Carson was leaving John got up and followed him out the door asking for a word.

"I just want to say I heard you talking with Jeannie earlier and thanks for not saying anything before Rodney wants too."

"It's perfectly fine lad, she shouldn't be poking around in other people's business."

"He is her brother though Carson."

"Aye, but that doesn't mean she can go poking around, she should wait until Rodney decides to tell her or she should confront him about it not go behind his back."

"Thanks anyway Carson it means a lot." Carson nodded and then made his way to his quarters with John heading back into his.

"What were you talking to Carson about?" Rodney asked when John entered the quarters once again. John debated for a minute whether he should tell Rodney but then decided he had a right to know.

"Earlier I went to find Jeannie to talk to her about what her problem is but when I found her she was talking to Carson. She wasn't ill or anything but she was asking questions about us, Carson denied everything and told her she should talk to you but she just stormed out of the room and back down to the lab. I was going to follow her to talk to her but Woolsey radioed and we left for the mission to find Lorne and I never thought anything more of it. But then you collapsed when we came through the gate, before we could even get to the infirmary. I sat there beside you for hours before I decided to go and confront her as she hadn't come down. When I found her in the lab she was talking to Radek and they were in the same conversation she had had with Carson. I pulled her aside and asked why she hadn't been to see you and she tried to lie to me by saying she had. I called her out on it and she turned the whole thing back around on me. I told her that it was up to you to tell her if you wanted to, and she should have at least come to infirmary. For all she knew you could have been dying. I know we agreed to talk to her when you were ready and we still can but I just got so angry that she didn't even come down to see if you were alright she didn't even radio she just pretended that she didn't know."

Rodney pulled John into a hug. "It's okay that you went to see her, I didn't expect you to but I'm not angry that you did. You did what you thought was right and god knows that I have done so much worse. I guess it just goes to show I don't really know Jeannie anymore do I? There was a time when she would be the first one at the hospital and wouldn't leave if I ended up there. I don't even know if it was the right thing to do anymore bringing her here. I thought that maybe we would be able patch our differences and get along but i really can't see how it will work."

"You could always assign her to a different science team or department, if it was that much trouble." John said trying to get a smile out of Rodney.

"I suppose we could." he replied. After their long and emotionally draining conversation they settled in for the night wondering what tomorrow would bring.

The next morning John was the first one up and got dressed leaving Rodney asleep as he had to rest for two days, he was almost out the door before he turned around and picked Rodney's laptop up off the coffee table. On his way to his office, John radioed Major Lorne and asked him to meet him there. He was just setting Rodney's laptop down on his desk when the door chimed; he opened it and let Evan in.

"Sir." Evan said when John was seated behind his desk.

"I need you to sort out the quarters for the crew of both the Daedalus and the Apollo, if we need to we can double some people up. The technicians from the both can go in the science quarters and obviously the military quarters for the marines with anyone else going into general quarters. If you do need to double up make sure Colonels Caldwell and Ellis have their own quarters. None of them need redecorating just make sure they have the right furniture in."

Evan nodded and left the office to start sorting it out. John sat in his office for a few hours doing paperwork before he decided to go and get changed so he could spar with Ronon. When he reached the quarters he could hear Rodney and Jeannie arguing.

"Since we have been here you have seen more of John and your team than you have me or Maddison Meredith!"

"That's because we work together Jeannie, we are friends you spend so long working together the way we do and you cannot help but be friends and don't call me Meredith you know I hate it."

"I'm sure John knows it too!"

"What on earth is that supposed to mean?"

"Did he tell you that he came to see me and basically lectured me the whole time and how dare he speak to me like that."

"Yes he told me he told me yesterday actually and John can speak to you the way he wants to he is the second in command and military commander of Atlantis he can pretty much do whatever he wants including lecturing you!"

"I don't care he won't do it again!"

"He can if he chooses and to be fair you deserved it Jeannie."

"What on earth is that supposed to mean?"

"I was in the infirmary for hours Jeannie and you didn't bother to visit! There was a time when you would have been the first there and the last to leave."

"How do you know?"

"John told me!"

"Of course John told you because you believe John don't you!"

"Why would John lie to me? He has no reason to!"

"How about that he is trying to come between us!"

"John wouldn't do that he is my best friend!"

"Yeah right best friend!"

"No, you're right its more than that. I love him and he has been there for me in the few years that we have been here more than what you have in our lives Jeannie. I truly am sorry that I prefer the company of him. But that's how i feel right now so just leave!" John didn't hear Jeannie reply but 'lantis told him that she was heading towards the door so back up a little and started walking towards the door and entered just as Jeannie was leaving. He received a dirty look of off her but he didn't care, he only cared about how Rodney was. When he entered their quarters Rodney was sitting on the sofa with a dejected look on his face.


	8. Chapter 8

"Hey" John said as he sat down next to him on the sofa.

"Hey" Rodney replied.

"How are you feeling?"

"Actually pretty alright. I guess you heard that?" he asked referring to the argument.

"Yeah, I am sorry."

"Its fine. Why are you back anyway?"

"I came to get changed to go spar with Ronon."

"Ah. Did you take my laptop?"

"No." John replied with a smirk on his face.

"You did, didn't you?" Rodney said while grinning

"I knew you would end up doing work and Carson specifically said no work, so I took it with me."

"Where is it now?"

"That I am not telling you." John said smiling.

"Come on, please?"

"Nope!" John said as he got up to get changed. He went to spar with Ronon and when he returned a few hours later he heard Rodney and Jeannie arguing again.

"We are your family Rodney you should care more about us than your friends!"

"Have you been there for me the last few years? No you haven't but John and everybody else have and I don't care if you are related by blood right now. You haven't done anything to show you care for me. You couldn't even visit the infirmary after I had collapsed! I could have been shot and then you ask my friends about me and John instead of just coming to ask me directly."

John entered the quarters and they both turned to face him "I think you should leave." he said without looking away from Rodney. He only knew she had left because he heard the swish of the doors closing behind her.

"Hey, are you okay?" John asked as he sat down next to Rodney.

"Yeah I am I promise."

"Okay" John replied knowing not to push Rodney or he wouldn't talk about it.

Later that night Carson stopped by again to check on Rodney.

"How are you feeling?" he asked.

"Fine." Rodney replied

"Okay. Tomorrow you can go back to work but just in the lab. You can't go off-world yet and I will tell John and Woolsey exactly the same thing."

"Thanks Carson and not just for this. John told me that Jeannie was asking you about us and he told me what you said to her. Thank you."

"It's alright; she shouldn't have been poking around in other people's business even if it is family."

On the way out Carson told John exactly what he had told Rodney in regards to Rodney's health. He also told John to keep an eye on Rodney and Jeannie as any stress on Rodney might cause his health to decline again. John waited for Rodney to fall asleep and then got up to head to the labs to find out if Jeannie was still there. When he arrived, Radek was the only one there and John asked where Jeannie had gone.

"She went to the mess hall to get some coffee, she should be back soon." Radek answered.

"Thanks Radek I'll go and find her." John replied. John left the lab and headed to the mess hall to find Jeannie on his way there he bumped into her in the hallway.

"Hey Jeannie can I talk to you for a minute?" he asked after he stopped her.

"I guess so." she replied and followed John to his office.

"So what do you want?" she asked when they were in and John had shut the door.

"I want you to lay off Rodney." he said bluntly.

"You do, do you?" she asked sarcastically.

"Yes because right now it is having an impact on his health ,and that can be bad for Atlantis and everyone here, including you, but also because I care about him and I hate to see what this is doing to him. If you cannot get along with Rodney and be nice just don't talk to him. As the military commander on this base I can send anyone back to Earth that poses a threat the safety of the people here, and if our head of science isn't at peak performance that sure as hell counts as putting the base in danger. Therefore, anyone who causes Rodney to be off game seriously, gets sent back to earth and then questioned by the SGC."

Jeannie just looked at John. "You know what, I don't care if you send us back to earth but Rodney is family and I can talk to him however I like. I don't care if it puts him in a bad mood but he needs to be told. He has to put family first!"

"Rodney considers most people on this base as him family and you may not be able to choose who your family are by blood but you can choose who you consider family. Here that means a hell of a lot more than blood as no one here will get to see their relatives again, you should count yourself lucky that you are here and that you still have Rodney. I could always send you back to Earth it's up to you, but stay away from Rodney for a while."

Jeannie glared at John before she stood up and went back to the lab. John completed some paperwork that was on his desk and then headed back to his quarters. He was sure that Rodney would be upset with him for his talk with Jeannie but they could deal with that in the morning.

The next morning John got up before Rodney woke up and headed out for a run with Ronon, by the time he got back, Rodney had left for the lab. John left for his office to prepare for the meeting he had with SG1 before lunch. At lunch time he met up with Rodney and the team in the mess.

"So what's everyone up to this afternoon?" John asked after he had sat down.

"More lab work." Rodney replied.

"Ronon and I plan to spar this afternoon. How about you?" Teyla asked while feeding Torren.

"I have a meeting with Lorne and SG1 or as they are now going to be called AR13" John said with a hint of distaste.

"They aren't going to like that. "Rodney said with a hint of smugness.

"Well they are going to have to deal with it, and I suppose they are not going to like having to follow major Lorne's orders either"

"They are definitely not going to like that considering they outrank him"

"Well Evan is second in command and the leader of AR2 so they are going to have to deal with that as well" John said.

"Would you be able to look after Torren once your meeting has ended?" Teyla asked.

"I would love to watch the little guy, do you want me to watch him while you spar?"

"Do you not have your meeting?"

"Yeah, but it will be fine." John picked up Torren and headed up to the conference room. Once there, he settled Torren on the floor and began getting ready for the meeting. Five minutes later Evan walked in and walked over to Torren.

"Hey little guy what are you doing here?" he asked.

"Well his mum and dad are sparring right now and I offered to watch him as Uncle Rodney is busy."

"No disrespect sir but you do know SG1 aren't going to like this" Evan said looking a little worried.

"Well they will have to deal with it won't they?" John said while shuffling through the papers he had in front of him. Evan was just telling him of their last mission when SG1 walked through the door.

"Major, Lieutenant Colonel" Sam said in way of greeting as they walked through the door. John and Evan nodded in return and sat down at the end of the conference table.

"Right then" John said and started the meeting.

"From now on you will be known collectively as AR13 and not SG1. Also I am military commander of the city and therefore you follow my orders and Major Lorne's, as he is second in command. This is regardless of any rank held above us am I clear?" he asked and looked around to see them all nodding.

"Right, as this is your first time through the gate in Pegasus, you will be joining Major Lorne and his team on a simple mission to a planet we have established trade links with. As you have never encountered the wraith before, if something goes wrong, you follow major Lorne's orders. On the mission you will be meeting the people of a local village, they will be wary of you at first as they have only dealt with Major Lorne's team and my own team. If you follow Major Lorne he will guide you through the proper greetings in the Pegasus galaxy and …" John never got to finish his sentence as his radio buzzed.

"Sheppard." he said and could hear Rodney's voice on the other end.

"John, we have a problem" he said

"Right give me two minutes I am on my way." he said to Rodney.

He turned to Evan "Major could you finish the debriefing, there is a problem and i am needed in the lab." he asked.

"Sure." Evan replied while John picked up Torren and quickly made his way down to the lab.

"Rodney, you radioed?" he asked.

"We have a problem. A hive ship just appeared above the city."


	9. Authors Note

So after long consideration i have decided to discontinue this story. I thank everyone who has left a review whether good or constructive, the fact that you took the time to review means a lot. Thanks to everyone who has followed and favourited the story, it also means a lot. I may decide to continue some time in the future but for the time being thank you for reading.


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